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- PDB-5m7y: Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clos... -

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Basic information

Entry
Database: PDB / ID: 5m7y
TitleCrystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannotriose
Components1,6-alpha-mannosidase
KeywordsHYDROLASE / Glycoside Hydrolase / Mannosidase / Carbohydrate
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
Metal-independent alpha-mannosidase / Metal-independent alpha-mannosidase (GH125) / DUF1237 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycoside hydrolase family 125 protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsMales, A. / Alonso-Gil, S. / Fernandes, P. / Williams, S.J. / Rovira, C. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Computational Design of Experiment Unveils the Conformational Reaction Coordinate of GH125 alpha-Mannosidases.
Authors: Alonso-Gil, S. / Males, A. / Fernandes, P.Z. / Williams, S.J. / Davies, G.J. / Rovira, C.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,6-alpha-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4144
Polymers50,8611
Non-polymers5533
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint8 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.414, 44.016, 85.079
Angle α, β, γ (deg.)90.000, 96.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 1,6-alpha-mannosidase


Mass: 50861.008 Da / Num. of mol.: 1 / Mutation: D220N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Strain: 13 / Type A / Gene: CPE0426 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8XNB2
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM MgCl2, 100 mM HEPES pH7.0, 27% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→51.82 Å / Num. obs: 263043 / % possible obs: 99.8 % / Redundancy: 4.1 % / CC1/2: 1 / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data reduction
Aimlessdata scaling
RefinementResolution: 1.55→51.82 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1801 3291 5.1 %RANDOM
Rwork0.147 ---
obs0.1487 64689 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.66 Å2 / Biso mean: 22.9027 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å2-0 Å2-0.19 Å2
2---0.73 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.55→51.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 36 293 3808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193719
X-RAY DIFFRACTIONr_bond_other_d00.023398
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.9525065
X-RAY DIFFRACTIONr_angle_other_deg3.6537888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90824.922193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73215648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2341515
X-RAY DIFFRACTIONr_chiral_restr0.1280.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024210
X-RAY DIFFRACTIONr_gen_planes_other0.0260.02873
X-RAY DIFFRACTIONr_mcbond_it1.8362.0551736
X-RAY DIFFRACTIONr_mcbond_other1.8362.0531735
X-RAY DIFFRACTIONr_mcangle_it2.4323.0742178
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 227 -
Rwork0.231 4528 -
all-4755 -
obs--99.62 %

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